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Use case example
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1. Create a folder for the result. We will create a new folder on the desktop called mb_results.
2. Open the Ananconda prompt and activate your macrobot environment if you are not already there.

``conda activate macrobot``

3. Macrobot is a command line program which requires the following arguments:

* source path (-s) - the path with the images coming from the Macrobot hardware system
* destination path (-d) - the path to store the results
* pathogen (-p) - which pathogen to predict ("mildew" or "rust")

4. For a test case we will use a test image set which will be automatically downloaded by the start of the software. To tell the software to use the test images, we will enter "test_images" for the source path -s argument

5. Start the software with the following command (adapt the destination path):

``mb -s test_images -d C:\Users\name\Desktop\mb_results\ -p mildew``

6. In your destination folder should appear all results:

* A csv file with the predicted values per leaf
* A report html file in folder report which allows and easy control over the pipeline.
* Images created by the software (white=pathogen, red=leaf detection, black=background)

If you want to use a real world experiments, make sure to provide the following folder structure with five images per plate:


| my_folder
| ├── experiment1
| │   ├── dai
|         └── plateID1
|             └── plateID1_backlight.tif
|             └── plateID1_green.tif
|             └── plateID1_blue.tif
|             └── plateID1_red.tif
|             └── plateID1_uvs.tif
| ├── experiment2
| │   ├── dai
|         └── plateID2
|             └── plateID2_backlight.tif
|             └── plateID2_green.tif
|             └── plateID2_blue.tif
|             └── plateID2_red.tif
|             └── plateID2_uvs.tif


Test image link:
https://doi.ipk-gatersleben.de/DOI/d92b5ec6-a83c-4ce6-99ab-ee4243764024/a9b2216b-4bb4-4300-8fc9-a259c485b236/2